@datagrok/bio 2.8.6 → 2.9.0

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.8.6",
+  "version": "2.9.0",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -34,14 +34,14 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.36.0",
+    "@datagrok-libraries/bio": "^5.37.0",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.39",
     "@datagrok-libraries/tutorials": "^1.3.6",
     "@datagrok-libraries/utils": "^4.0.17",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
-    "datagrok-api": "^1.13.3",
+    "datagrok-api": "^1.16.0",
     "dayjs": "^1.11.4",
     "fastest-levenshtein": "^1.0.16",
     "openchemlib": "6.0.1",

package/src/package-test.ts

@@ -28,6 +28,7 @@ import './tests/to-atomic-level-tests';
 import './tests/mm-distance-tests';
 import './tests/activity-cliffs-tests';
 import './tests/sequence-space-test';
+import './tests/scoring';
 
 
 export const _package = new DG.Package();

package/src/package-types.ts

@@ -14,7 +14,6 @@ export const enum BioPackagePropertiesNames {
 
 
 export class BioPackageProperties extends Map<string, any> {
-
   private _onPropertyChanged: Subject<string> = new Subject<string>();
   public get onPropertyChanged(): Observable<string> { return this._onPropertyChanged; }
 

package/src/package.ts

@@ -21,7 +21,7 @@ import {removeEmptyStringRows} from '@datagrok-libraries/utils/src/dataframe-uti
 
 import {SequenceSimilarityViewer} from './analysis/sequence-similarity-viewer';
 import {SequenceDiversityViewer} from './analysis/sequence-diversity-viewer';
-import {substructureSearchDialog} from './substructure-search/substructure-search';
+import {SubstructureSearchDialog} from './substructure-search/substructure-search';
 import {saveAsFastaUI} from './utils/save-as-fasta';
 import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
 import {delay} from '@datagrok-libraries/utils/src/test';
@@ -40,10 +40,11 @@ import {
   getLibFileNameList,
   getLibraryPanelUI
 } from './utils/monomer-lib';
-import {getMacromoleculeColumn} from './utils/ui-utils';
+import {getMacromoleculeColumns} from './utils/ui-utils';
 import {DimReductionMethods, ITSNEOptions, IUMAPOptions} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {SequenceSpaceFunctionEditor} from '@datagrok-libraries/ml/src/functionEditors/seq-space-editor';
 import {ActivityCliffsFunctionEditor} from '@datagrok-libraries/ml/src/functionEditors/activity-cliffs-editor';
+import {SCORE, calculateScores} from '@datagrok-libraries/bio/src/utils/macromolecule/scoring';
 
 import {demoBio01UI} from './demo/bio01-similarity-diversity';
 import {demoBio01aUI} from './demo/bio01a-hierarchical-clustering-and-sequence-space';
@@ -602,7 +603,7 @@ export function importBam(fileContent: string): DG.DataFrame [] {
 //top-menu: Bio | Convert | Notation...
 //name: convertDialog
 export function convertDialog() {
-  const col = getMacromoleculeColumn();
+  const col = getMacromoleculeColumns()[0];
   convert(col);
 }
 
@@ -734,12 +735,52 @@ export function diversitySearchTopMenu() {
   view.dockManager.dock(viewer, 'down');
 }
 
-//top-menu: Bio | Search | Substructure...
-//name: bioSubstructureSearch
-//description: Finds sequence with the given subsequence
-export function bioSubstructureSearch(): void {
-  const col = getMacromoleculeColumn();
-  substructureSearchDialog(col);
+//name: SearchSubsequenceEditor
+//tags: editor
+//input: funccall call
+export function searchSubsequenceEditor(call: DG.FuncCall) {
+  const columns = getMacromoleculeColumns();
+  if (columns.length === 1)
+    call.func.prepare({macromolecules: columns[0]}).call(true);
+  else
+    new SubstructureSearchDialog(columns);
+}
+
+//top-menu: Bio | Search | Subsequence...
+//name: Subsequence Search
+//input: column macromolecules
+//editor: Bio:SearchSubsequenceEditor
+export function SubsequenceSearchTopMenu(macromolecules: DG.Column): void {
+  grok.shell.tv.getFiltersGroup({createDefaultFilters: false}).updateOrAdd({
+    type: 'Bio:bioSubstructureFilter',
+    column: macromolecules.name,
+    columnName: macromolecules.name,
+  });
+  grok.shell.tv.grid.scrollToCell(macromolecules, 0);
+}
+
+//top-menu: Bio | Caclulate | Identity...
+//name: Identity Scoring
+//description: Adds a column with fraction of matching monomers
+//input: dataframe table [Table containing Macromolecule column]
+//input: column macromolecules {semType: Macromolecule} [Sequences to score]
+//input: string reference [Sequence, matching column format]
+//output: column scores
+export async function sequenceIdentityScoring(table: DG.DataFrame, macromolecule: DG.Column, reference: string): Promise<DG.Column<number>> {
+  const scores = calculateScores(table, macromolecule, reference, SCORE.IDENTITY);
+  return scores;
+}
+
+//top-menu: Bio | Caclulate | Similarity...
+//name: Similarity Scoring
+//description: Adds a column with similarity scores, calculated as sum of monomer fingerprint similarities
+//input: dataframe table [Table containing Macromolecule column]
+//input: column macromolecules {semType: Macromolecule} [Sequences to score]
+//input: string reference [Sequence, matching column format]
+//output: column scores
+export async function sequenceSimilarityScoring(table: DG.DataFrame, macromolecule: DG.Column, reference: string): Promise<DG.Column<number>> {
+  const scores = calculateScores(table, macromolecule, reference, SCORE.SIMILARITY);
+  return scores;
 }
 
 //name: saveAsFasta

package/src/substructure-search/substructure-search.ts

@@ -17,64 +17,93 @@ export const enum MONOMERIC_COL_TAGS {
 
 const SUBSTR_HELM_COL_NAME = 'substr_helm';
 
-/**
- * Searches substructure in each row of Macromolecule column
- *
- * @param {DG.column} col Column with 'Macromolecule' semantic type
- */
-export function substructureSearchDialog(col: DG.Column<string>): void {
-  const units = col.getTag(DG.TAGS.UNITS);
-  const separator = col.getTag(bioTAGS.separator);
-  // const notations = [NOTATION.FASTA, NOTATION.SEPARATOR, NOTATION.HELM];
-
-  const substructureInput = ui.textInput('Substructure', '');
-
-  const editHelmLink = ui.link('Edit helm', async () => {
-    updateDivInnerHTML(inputsDiv, grid.root);
-    await ui.tools.waitForElementInDom(grid.root);
-    setTimeout(() => {
-      grid.cell(SUBSTR_HELM_COL_NAME, 0).element.children[0].dispatchEvent(
-        new KeyboardEvent('keydown', {key: 'Enter'}));
-    }, 100);
-  });
+export class SubstructureSearchDialog {
+  units: string;
+  separator: string;
+  inputsDiv: HTMLDivElement;
+  substructureInput: DG.InputBase<string>;
+  separatorInput: DG.InputBase<string>;
+  editHelmLink: HTMLAnchorElement;
+  columnsInput: DG.InputBase<DG.Column | null>;
+  grid: DG.Grid;
+  col: DG.Column;
+  dialog: DG.Dialog;
+
+  constructor(columns: DG.Column<string>[]) {
+    this.col = columns[0];
+    this.createUI();
+  }
+
+  editHelmLinkAction(): void {
+    updateDivInnerHTML(this.inputsDiv, this.grid.root);
+    ui.tools.waitForElementInDom(this.grid.root).then(() => {
+      setTimeout(() => {
+        this.grid.cell(SUBSTR_HELM_COL_NAME, 0).element.children[0].dispatchEvent(
+          new KeyboardEvent('keydown', {key: 'Enter'})
+        );
+      }, 100);
+    });
+  }
+
+  updateInputs(): void {
+    const selectedInput = this.units === NOTATION.HELM ? ui.divV([this.columnsInput, this.editHelmLink]) :
+      this.units === NOTATION.SEPARATOR ? ui.inputs([this.columnsInput, this.substructureInput, this.separatorInput]) :
+        ui.inputs([this.columnsInput, this.substructureInput]);
 
-  const df = DG.DataFrame.create(1);
-  df.columns.addNewString(SUBSTR_HELM_COL_NAME).init((_i) => '');
-  df.col(SUBSTR_HELM_COL_NAME)!.semType = col.semType;
-  df.col(SUBSTR_HELM_COL_NAME)!.setTag(DG.TAGS.UNITS, NOTATION.HELM);
-  const grid = df.plot.grid();
-  const separatorInput = ui.textInput('Separator', separator);
-
-  const inputsDiv = ui.div();
-
-  const inputs = units === NOTATION.HELM ? ui.divV([editHelmLink]) :
-    units === NOTATION.SEPARATOR ? ui.inputs([substructureInput, separatorInput]) :
-      ui.inputs([substructureInput]);
-
-  updateDivInnerHTML(inputsDiv, inputs);
-
-  ui.dialog('Substructure Search')
-    .add(ui.divV([
-      ui.divText(`Notation: ${units}`),
-      inputsDiv,
-    ]))
-    .onOK(async () => {
-      let substructure = units === NOTATION.HELM ? df.get(SUBSTR_HELM_COL_NAME, 0) : substructureInput.value;
-      if (units === NOTATION.SEPARATOR && separatorInput.value !== separator && separatorInput.value !== '')
-        substructure = substructure.replaceAll(separatorInput.value, separator);
-      const matchesColName = `Matches: ${substructure}`;
-      const colExists = col.dataFrame.columns.names()
-        .filter((it) => it.toLocaleLowerCase() === matchesColName.toLocaleLowerCase()).length > 0;
-      if (!colExists) {
+    updateDivInnerHTML(this.inputsDiv, selectedInput);
+  }
+
+  updateNotationDiv(): void {
+    this.units = this.col.getTag(DG.TAGS.UNITS);
+    this.separator = this.col.getTag(bioTAGS.separator);
+    const notationDiv = this.dialog.root.getElementsByClassName('notation-text')[0];
+    if (notationDiv)
+      notationDiv.textContent = `Notation: ${this.units}`;
+  }
+
+  createUI(): void {
+    const dataframe = grok.shell.tv.dataFrame;
+    const seqColOptions = {filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE};
+    this.columnsInput = ui.columnInput('Column', dataframe, this.col, (column: DG.Column) => {
+      this.col = column;
+      this.updateNotationDiv();
+      this.updateInputs();
+    }, seqColOptions);
+
+    this.substructureInput = ui.stringInput('Substructure', '');
+
+    this.editHelmLink = ui.link('Edit helm', () => this.editHelmLinkAction(), undefined, {style: {position: 'relative', left: '95px'}});
+
+    const df = DG.DataFrame.create(1);
+    df.columns.addNewString(SUBSTR_HELM_COL_NAME).init((_i) => '');
+    df.col(SUBSTR_HELM_COL_NAME)!.semType = this.col.semType;
+    df.col(SUBSTR_HELM_COL_NAME)!.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+    this.grid = df.plot.grid();
+    this.separatorInput = ui.stringInput('Separator', this.separator);
+
+    this.inputsDiv = ui.div();
+    this.units = this.col.getTag(DG.TAGS.UNITS);
+    this.separator = this.col.getTag(bioTAGS.separator);
+    this.updateInputs();
+
+    this.dialog = ui.dialog('Substructure Search')
+      .add(ui.divV([
+        ui.divText(`Notation: ${this.units}`, 'notation-text'),
+        this.inputsDiv,
+      ]))
+      .onOK(async () => {
+        let substructure = this.units === NOTATION.HELM ? df.get(SUBSTR_HELM_COL_NAME, 0) : this.substructureInput.value;
+        if (this.units === NOTATION.SEPARATOR && this.separatorInput.value !== this.separator && this.separatorInput.value !== '')
+          substructure = substructure.replaceAll(this.separatorInput.value, this.separator);
         let matches: DG.BitSet;
-        if (units === NOTATION.HELM)
-          matches = await helmSubstructureSearch(substructure, col);
+        if (this.units === NOTATION.HELM)
+          matches = await helmSubstructureSearch(substructure, this.col);
         else
-          matches = linearSubstructureSearch(substructure, col);
-        col.dataFrame.columns.add(DG.Column.fromBitSet(matchesColName, matches));
-      } else { grok.shell.warning(`Search ${substructure} is already performed`); }
-    })
-    .show();
+          matches = linearSubstructureSearch(substructure, this.col);
+        this.col.dataFrame.filter.and(matches);
+      })
+      .show();
+  }
 }
 
 export function linearSubstructureSearch(substructure: string, col: DG.Column<string>, separator?: string): DG.BitSet {

package/src/tests/activity-cliffs-tests.ts

@@ -47,5 +47,5 @@ category('activityCliffs', async () => {
     viewList.push(actCliffsTableViewWithEmptyRows);
 
     await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, 3, DimReductionMethods.UMAP, 'sequence');
-  });
+  }, {skipReason: 'GROK-13851: Unhandled exceptions'});
 });

package/src/tests/detectors-tests.ts

@@ -274,13 +274,13 @@ MWRSWY-CKHP`;
     await _testDf(readSamples(Samples.fastaCsv), {
       'Sequence': new PosCol(NOTATION.FASTA, ALIGNMENT.SEQ, ALPHABET.PT, 20, false),
     });
-  });
+  }, {skipReason: 'GROK-13851: Unhandled exceptions'});
 
   test('samplesFastaFasta', async () => {
     await _testDf(readSamples(Samples.fastaFasta), {
       'sequence': new PosCol(NOTATION.FASTA, ALIGNMENT.SEQ, ALPHABET.PT, 20, false),
     });
-  });
+  }, {skipReason: 'GROK-13851: Unhandled exceptions'});
 
   // peptidesComplex contains monomers with spaces in AlignedSequence columns, which are forbidden
   // test('samplesPeptidesComplexPositiveAlignedSequence', async () => {

package/src/tests/scoring.ts

@@ -0,0 +1,38 @@
+import * as DG from 'datagrok-api/dg';
+
+import {category, test, expectFloat, before} from '@datagrok-libraries/utils/src/test';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {sequenceIdentityScoring, sequenceSimilarityScoring} from '../package';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+
+category('Scoring', () => {
+  const sequence = 'sequence';
+  const expectedSimilarity = 'expected_similarity';
+  const expectedIdentity = 'expected_identity';
+  const table = DG.DataFrame.fromCsv(`${sequence},${expectedSimilarity},${expectedIdentity}
+  PEPTIDE1{Aca.Orn.gGlu.Pqa.D-His_1Bn.dH.hHis.4Abz.D-Tic.D-Dap.Y.Iva.meS.F.P.F.D-1Nal}$$$$,1.0,1.0
+  PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.68,0.53
+  PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.34,0.0
+  `);
+  const seqCol: DG.Column<string> = table.getCol(sequence);
+  seqCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+  seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+  const reference = seqCol.get(0)!;
+
+  before(async () => {
+    const monomerLibHelper = await getMonomerLibHelper();
+    await monomerLibHelper.loadLibraries(true);
+  });
+
+  test('Identity', async () => {
+    const scoresCol = await sequenceIdentityScoring(table, seqCol, reference);
+    for (let i = 0; i < scoresCol.length; i++)
+      expectFloat(scoresCol.get(i)!, table.get(expectedIdentity, i), 0.01, `Wrong identity score for sequence at position ${i}`);
+  });
+
+  test('Similarity', async () => {
+    const scoresCol = await sequenceSimilarityScoring(table, seqCol, reference);
+    for (let i = 0; i < scoresCol.length; i++)
+      expectFloat(scoresCol.get(i)!, table.get(expectedSimilarity, i), 0.01, `Wrong similarity score for sequence at position ${i}`);
+  });
+});

package/src/utils/cell-renderer.ts

@@ -26,6 +26,7 @@ import * as C from './constants';
 
 import {_package, getBioLib} from '../package';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 
 
 type TempType = { [tagName: string]: any };
@@ -292,14 +293,15 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
     const cell = gridCell.cell;
     const tableCol = gridCell.tableColumn as DG.Column<string>;
     const s: string = cell.value ?? '';
+    const separator = tableCol.tags[bioTAGS.separator];
+    const units: string = tableCol.tags[DG.TAGS.UNITS];
     w = getUpdatedWidth(grid, g, x, w);
     //TODO: can this be replaced/merged with splitSequence?
     const [s1, s2] = s.split('#');
-    const uh = UnitsHandler.getOrCreate(tableCol);
-    const splitter = uh.getSplitter();
+    const splitter = getSplitter(units, separator);
     const subParts1 = splitter(s1);
     const subParts2 = splitter(s2);
-    drawMoleculeDifferenceOnCanvas(g, x, y, w, h, subParts1, subParts2, uh.units);
+    drawMoleculeDifferenceOnCanvas(g, x, y, w, h, subParts1, subParts2, units);
   }
 }
 

package/src/utils/ui-utils.ts

@@ -1,13 +1,13 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-export function getMacromoleculeColumn(): DG.Column | any {
-  const col = grok.shell.t.columns.bySemType(DG.SEMTYPE.MACROMOLECULE);
-  if (col === null) {
+export function getMacromoleculeColumns(): DG.Column<any>[] | any {
+  const columns = grok.shell.t.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
+  if (columns === null) {
     grok.shell.error('Current table does not contain macromolecules');
     return;
   }
-  return col;
+  return columns;
 }
 
 export function updateDivInnerHTML(div: HTMLElement, content: string | Node): void {